High Evolutionary Dynamism in 5S rDNA of Fish: State of the Art

Abstract

The 5S ribosomal DNA (rDNA) consists of one transcriptional unit of about 120 base pairs, which is separated from the next unit by a non-transcribed spacer (NTS). The coding sequence and the NTS together form a repeat unit which can be found in hundreds to thousands of copies tandemly repeated in the genomes. The NTS regions seem to be subject to rapid evolution. The first general model of evolution of these multigene families was referred to as divergent evolution, based on studies using hemoglobin and myoglobin as model systems. Later studies showed that nucleotide sequences of different multigene family members are more closely related within species than between species. This observation led to a new model of multigene family evolution, termed concerted evolution. Another model of evolution, named the birth-and-death model, has been found to be more suitable to explain the long-term evolution of these multigene families. According to this model, new genes originate by successive duplications, and these new genes are either maintained for a long time or are lost, or else degenerate into pseudogenes. In this review we describe different sources of variability in the 5S rDNA genes observed in several distinct fish species. This variability is mainly referred to NTSs and includes the presence of other multigene families (mainly LINEs, SINEs, non-LTR retrotransposons, and U snRNA families). Different types of microsatellites have also been found to contribute to the increase of variability in this region. Our recent results suggest that horizontal transfer contributes to the increase of diversity in the NTSs of some species. Variability in the 5S rDNA coding region affecting the stability of the structure, but without effects on the function of the 5S rRNA, is also described. Retrotransposons seem to be responsible for the high dynamism of 5S rDNA, while microsatellites acting as recombination hot spots could stabilize a wide variety of unusual DNA structures, affecting DNA replication and enhancing or decreasing promoter activity in gene expression. The relationship between the high variability found at molecular level and the low variability found at chromosomal level is also discussed.

Linking maternal and somatic 5S rRNA types with different sequence-specific non-LTR retrotransposons

“…Additionally, the absence and presence of Mutsu retrotransposon RNA and piRNA in eggs, respectively, together with the reversed situation in adult tissue, fuel the need to investigate the obvious link between 5S rRNA and these sequence-specific non-LTR retrotransposons. All of this sparks the notion that the retrotransposon elements are involved in the way the copy numbers evolved in both maternal-and somatic-type 5S rDNA loci (Rebordinos et al 2013), similar to that reported in 45S (Symonová et al 2013).…”

“…If we assume that two intact ORFs equals a functional retrotransposon element, it is an intriguing observation that apparently in the locus with many (maternal-type) 5S rRNA genes, several potentially active retrotransposons reside, whereas in the small (somatic-type) locus there is none. It raises the question whether these retrotransposons were evolutionarily involved in achieving and maintaining the needed high maternal-type 5S rDNA gene copy number, as well as the limited somatictype 5S rRNA gene copy (Cioffi et al 2010;Rebordinos et al 2013). In this scenario, one function of the sequence difference between maternal-and somatic-type 5S rRNA genes could be that the different target sequence in the somatictype genes obstructs new integration of retrotransposons, thus stabilizing the somatic-type 5S rRNA locus.…”

Isolation and characterization of 5S rDNA sequences in catfishes genome (Heptapteridae and Pseudopimelodidae): perspectives for rDNA studies in fish by C0t method

“…Thus, presence of other multigene families (LINES, SINES, non-LTR retrotransposons), especially regarding the NTSs, appears to be suitable among fish. These multigene families seems to collaborate with variability in this region (seem review Rebordinos et al 2013).…”

The Organization of Repetitive DNA in the Genomes of Amazonian Lizard Species in the Family Teiidae

“…Ribosomal RNA genes are among the best known multigene families in vertebrates, and the molecular variability of the 5S rDNA has been elucidated frequently according to NTS, which are normally associated with other repetitive DNA [Campo and García-Vázquez, 2012;Rebordinos et al, 2013]. In the species Cnemidophorus sp.…”